Normalization of Enzyme Expression and Activity Regulating Vitamin A Metabolism Increases RAR-Beta Expression and Reduces Cellular Migration and Proliferation in Diseases Caused by Tuberous Sclerosis Gene Mutations

Background Mutation in a tuberous sclerosis gene (TSC1 or 2) leads to continuous activation of the mammalian target of rapamycin (mTOR). mTOR activation alters cellular including vitamin A metabolism and retinoic acid receptor beta (RARβ) expression. The goal of the present study was to investigate the molecular connection between vitamin A metabolism and TSC mutation. We also aimed to investigate the effect of the FDA approved drug rapamycin and the vitamin A metabolite retinoic acid (RA) in cell lines with TSC mutation. Methods Expression and activity of vitamin A associated metabolic enzymes and RARβ were assessed in human kidney angiomyolipoma derived cell lines, primary lymphangioleiomyomatosis (LAM) tissue derived LAM cell lines. RARβ protein levels were also tested in primary LAM lung tissue sections. TaqMan arrays, enzyme activities, qRT-PCRs, immunohistochemistry, immunofluorescent staining, and western blotting were performed and analysed. The functional effects of retinoic acid (RA) and rapamycin were tested in a scratch and a BrDU assay to assess cell migration and proliferation. Results Metabolic enzyme arrays revealed a general deregulation of many enzymes involved in vitamin A metabolism including aldehyde dehydrogenases (ALDHs), alcohol dehydrogenases (ADHs) and Cytochrome P450 2E1 (CYP2E1). Furthermore, RARβ downregulation was a characteristic feature of all TSC-deficient cell lines and primary tissues. Combination of the two FDA approved drugs -RA for acute myeloid leukaemia and rapamycin for TSC mutation- normalised ALDH and ADH expression and activity, restored RARβ expression and reduced cellular proliferation and migration. Conclusion Deregulation of vitamin A metabolizing enzymes is a feature of TSC mutation. RA can normalize RARβ levels and limit cell migration but does not have a significant effect on proliferation. Based on our data, translational studies could confirm whether combination of RA with reduced dosage of rapamycin would have more beneficial effects to higher dosage of rapamycin monotherapy meanwhile reducing adverse effects of rapamycin for patients with TSC mutation.

Conclusion: Deregulation of vitamin A metabolizing enzymes is a feature of TSC mutation. RA can normalize RARb levels and limit cell migration but does not have a significant effect on proliferation. Based on our data, translational studies could confirm whether combination of RA with reduced dosage of rapamycin would have more beneficial effects to higher dosage of rapamycin monotherapy meanwhile reducing adverse effects of rapamycin for patients with TSC mutation.
Keywords: tuberous sclerosis gene mutation, RARb, vitamin A metabolism, retinoic acid, rapamycin BACKGROUND Tuberous sclerosis, angiomyolipoma and lymphangioleiomyomatosis (LAM) are diseases characterised by slow growing tumours that are affecting many parts of the body (1,2) including the skin, brain, kidneys and the lungs. The above diseases are caused by the mutation of tumour suppressor genes tuberous sclerosis 1 or 2 (TSC or TSC2) (1). The above tumours were initially considered benign, but angiomyolipoma and LAM have recently been reclassified as "low grade, destructive, metastasizing neoplasms" characterised by asmooth muscle actin (a-SMA), vimentin, desmin and melanoma gp100 (HMB45) markers. Diseases caused by TSC mutations bear all the hallmarks of cancers including genetic mutations, evasion of growth suppression, resistance to cell death, metabolic reprogramming to avoid immune detection, and capability of invasion (3). Loss of TSC activity results in continuous activation of the mTOR pathway, which is also characteristic to various neoplasms where upstream mutations or signalling malfunction both result in mTOR activation (4). mTOR activation alters various cellular functions including cellular proliferation, autophagy, mitochondrial biogenesis, and cellular metabolism. Activation of the mTOR pathway can change anabolic cell growth processes such as protein and lipid synthesis in correlation with external growth factor or nutrient intake (5). In our previous study of LAM, apart from detecting morphological abnormalities in mitochondria and suppression of ROS production, we identified downregulation of the proliferation suppressor nuclear receptors of the retinoic acid gene family both retinoic acid receptor (RAR) and retinoid x receptor (RXR) as well as several miRNA-s that regulate RAR expression including miR29b (6). RAR and RXR are receptors of retinoic acid (RA), a metabolite of vitamin A (7). Both classes of nuclear receptors have three subtypes (a, b, and g) and in-patient derived LAM cell lines RARb mRNA expression was found significantly reduced (6). Interestingly, RARb is the receptor that is associated with the antitumour effects of RA (8)(9)(10). In many neoplastic diseases, expression of RARb is often downregulated or lost indicating that RARb plays an important role in tumour suppression (11). RA is a metabolite of the lipophilic vitamin A (retinol) which is obtained from plant or animal sources in the form of carotenoids and retinyl esters, respectively (12). RA is a lipophilic molecule with three isoforms: all-trans, 9-cis and 13-cis RA and is stored in forms of retinyl esters primarily in the liver as well as the kidneys, lungs and the bone marrow (12,13). In circulation, retinol is bound to retinol-binding protein (RBP) which enters the cells through RBP receptors (STRA6) (12). In the cells, retinol-dehydrogenase (RDH) or alcohol-dehydrogenase (ADH) oxidize retinol to retinal which is irreversibly converted to RA by the aldehyde dehydrogenase (ALDH) family also known as retinaldehyde dehydrogenase (RALDH) (12). RA binds to cellular retinoic acid-binding protein (CRABP) in the cell that carries RA into the nucleus where it binds to nuclear RARs to function as transcription factors. RA signalling is dependent upon its nuclear availability, controlled among others by RBP1, which is the carrier protein involved in the transport of retinol from the storage site to peripheral tissues (12). Interestingly, the administration of RA not only activates the transcription factor RARb but also increases its expression (14,15). As currently the only FDA approved drug to treat angiomyolipoma, tuberous sclerosis or LAM is rapamycin, search for additional therapeutic targets is important. Especially so, as rapamycin can only slow down disease progression and cannot offer a cure. Additionally, rapamycin has significant side effects therefore not all patients can tolerate the treatment (16,17). Discontinuation of rapamycin, however, leads to rapid disease progression (17). Tissues affected by TSC mutation are low in RARb expression (18,19). As, RARb is regulated by RA (6,(19)(20)(21), a product of vitamin A metabolism, we theorised that not just RARb expression is low in LAM, but it is likely that enzymes of vitamin A metabolism malfunction. To test the theory vitamin A metabolic enzyme expression and activity was tested. Simultaneously, the effect of the metabolic product RA was assessed in cell migration and proliferation alone or in combination with rapamycin using TSC mutant cell lines.
Based on our results, such combination of rapamycin with RA might offer a novel therapeutic strategy if our in vitro data could be confirmed in a clinical study.
Haematoxylin Eosin Staining 5 µm thick tissue sections of primary normal and LAM lungs (n=6 each, respectively) were stained in Mayer's haematoxylin solution (Sigma-Aldrich, St. Louis, USA) for 10 min, washed, then differentiated with 0.25% acetic acid and in eosin solution. Sections were mounted using Vectashield mounting medium (Vector Laboratories, Burlingame, USA). Images were taken using Nikon Eclipse Ti-U inverted microscope.

Immunofluorescent Staining
Normal, BSMC, NHLF, LAM (four individual cell lines), S103 (TSC2+/+) and S102 (TSC2-/-) cells were cultured for 3 days using Falcon ™ chambered cell culture slides (Thermo Fisher Scientific, Waltham, USA). Cell cultures were then fixed with 4% formaldehyde and permeabilized with PBS containing 0.1% Triton-X and 5% BSA. Slides were incubated with primary antibodies ( Table 1) overnight at 4°C. Slides were washed with TBS for three times then incubated with corresponding secondary antibody ( Table 1) for 90 min at RT. Nuclei were counter stained with DAPI. Images were acquired using an Olympus IX-81 (OLYMPUS Corporation, Tokyo, Japan) both light and fluorescence microscope. Immunohistochemistry 5 µm thick tissue sections of primary normal and LAM lungs were stained using immunohistochemistry. First, the slides were rinsed in heated xylene and were washed with a descending series of alcohol to remove paraffin. After deparaffination the slides were rehydrated in distilled water and antigen retrieval was performed by heating the slides in Target Retrieval Solution (pH 6, DAKO, Produktionsvej, Denmark) at 97°C for 20-30 min. Subsequently slides were washed in dH 2 O and endogenous peroxidase activity was blocked with 3% H 2 O 2 containing TBS (pH 7.4) for 15 min. Then slides were washed three times with TBS containing Tween (0.05%, pH 7.4). Preblocking was carried out with 3% BSA in TBS for 20 min before overnight incubation with anti-Melanoma gp100 antibody (HMB-45) (1:100, HMB-45 mouse monoclonal antibody clone: Ab787, ABcam) and anti-RARb (1:100, anti-RARb rabbit monoclonal Rapamycin and Retinoic Acid (RA) Treatments BSMC, NHLF, LAM (four individual cell lines), S103 (TSC2+/+) and S102 (TSC2-/-) cell cultures were treated with rapamycin and/or RA. The two drugs were used in the following concentrations: 10 or 20 nM rapamycin catalogue: tlrl-rap (InvivoGen, San Diego, USA) and 1 or 2 µM RA (Sigma-Aldrich, St. Louis, USA) for 24h at 37°C, 5% CO 2 .

Western Blot
Cells were lysed in ice-cold RIPA buffer (Sigma-Aldrich, St. Louis, USA) supplemented with protease inhibitors (Roche Diagnostics, Mannheim, Germany) for 30 min on ice and centrifuged at 16,000 × g for 20 min at 4°C. The supernatant was then used as the cell lysate. The protein content of each cell lysate was assessed using a Qubit protein assay kit (Thermo Scientific, Waltham, MA). 30 µg of total protein was loaded onto Mini Protean gel (Bio-Rad, California, USA), then electrophoresis was followed by overnight blotting onto a nitrocellulose membrane using 10 mA current. The blots then were blocked in 5% non-fat skimmed milk blocking solution (Bio-Rad, California, USA) in TBS-T buffer for 1 h and incubated with primary antibodies ( Quantitative qRT-PCR qRT-PCR was performed using SensiFAST SYBR Green reagent (BioLine, London, UK) in an ABI StepOnePlus system. Gene expressions using sequence specific primers (S.

Wound Healing Assay
Cells were grown to 90% confluence in 24 well plates and wound gap was made by scratching the cell with rapamycin (10 nM), RA (2 mM) and rapamycin (10 nM) + RA (2 mM) was after inducing the wound gap. The healing of the wound gap by cell migration and the centre of the gap was monitored with images taking with EVOS light microscopy (Thermo Fisher Scientific, Waltham, USA) and the gap area was quantified using ImageJ software.
BrdU Click-Ti Proliferation Assay S103 and S102 cells were cultured using Falcon ™ chambered cell culture slides (Thermo Fisher Scientific, Waltham, USA

3D Co-Cultures
3D aggregates were formed as described previously (27,28). Briefly, normal human lung fibroblasts (NHLF) and bronchial smooth muscle cells (BSMC) were isolated from anonymous donors of different ages and sexes and were purchased from Lonza (Basel, Switzerland). All cells were cultured at 37°C and 5% CO2 in primary cell culture media. NHLF, BSMC and LAM cell types were sub-cultured and mixed at 1:1 ratio then dispensed 3*105 cells/well onto a low-attachment 96-well Ubottom plates (Corning, New York, USA). The 3D aggregate cocultures were incubated in the presence or absence of 10 nM rapamycin and/or 2 mM RA for 24 h, then collected into cryomold and sectioned for staining.

Statistical Analysis
Unless otherwise noted, statistical analysis was performed with SPSS version 20 software. S102 and S103 data are presented as mean ± technical error of three replicates and statistical analysis was performed using student t-test. In experiments using primary LAM lung derived cell lines and their controls (an average of BSMC n=4 and NHLF n=4 samples) data are presented as mean ± standard error of mean (SEM), and statistical analysis was performed using the one-way ANOVA. p<0.05 was considered as significant.

RESULTS
To investigate the involvement of the enzyme cascades associated with vitamin A metabolism in TSC deficient cells, human enzyme profiler arrays (RT2 PCR) were used to compare mRNA levels of specific enzymes in the human kidney angiomyolipoma cell line S102 (TSC2-/-) and its control S103 (TSC2+/+). Out of the alcohol dehydrogenase family, four enzymes (ADH1A, ADH1B, ADH1C and ADH6) were significantly upregulated and one enzyme was downregulated (ADH4) in the mutant cell line ( Figure 1A). In the aldehyde dehydrogenase family three enzymes (ALDH1A2, ALDH1A3, and ALDH3A1) were upregulated, while five enzymes were downregulated (ALDH1A1, ALDH3B1, ALDH3B2, ALDH4A1 and ALDH5A1) ( Figure 1A). Additionally, analysis of the array data showed significant increase in CYP2E1 mRNA level ( Figure 1A, S. Table 2). To predict the connection (expression, physical interaction, co-localization, etc) amongst the above  Table 3). ADHs and ALDHs -especially ADH4, ALDH1A2 and ALDH1A3-were predicted to physically interact with molecules involved in the RA metabolic process and RARb binding ( Figure 1B). To determine whether ADHs and ALDHs are present in TSC2-deficient LAM cells, ADHs and ALDHs mRNA expression levels were quantified by qRT-PCR in four patient derived LAM cell lines and normal individual primary human bronchial smooth muscle cell (BSMC) as well as primary normal human lung fibroblast cells (NHLF) as controls (S. Figure 1). Just as in the TSC2-/-angiomyolipoma cell line S102, in the primary LAM lung tissue derived cell lines the expression of ADH1, ADH4 and ALDH1A1-2-3 showed the same pattern ( Figure 1C). Apart from vitamin A metabolism, the importance of ALDH and ADH were demonstrated in cancer cell proliferation, motility and metastasis (30,31), due to their specific role in affecting mTOR dependent signalling. In a previous study it has been revealed that ALDH1A3 downregulation directly affects mTOR expression and its downstream signals via S6K (32). Result that ALDH1A3 mRNA was significantly upregulated in TSC2-/-S102 and patient derived LAM lung cell lines that leads to mTOR activation and downregulation of RARb expression (6) was confirmed by immunofluorescent staining ( Figure 1D) and western blotting ( Figure 1E). To confirm the cell line data, primary normal and LAM lung tissue sections (n=6) were stained for RARb protein by immunohistochemistry ( Figure 1F, S. Figure 2). The staining of primary LAM tissues confirmed that reduced expression of RARb expression in the structural cells of the lung tissue is a feature of the TSC mutant LAM lungs ( Figure 1F). As RA is known to upregulate RARb expression (14,15), we set out to investigate whether RA could restore normal levels of RARb in TSC2-/-cell lines. Four patient derived LAM lung cell lines were treated with 1 mM or 2 mM (33, 34) RA for 24 h, then RARb expression was quantified using qRT-PCR ( Figure 2A) and immunofluorescent staining ( Figures 2B, C). Following incubation with 2 mM RA, RARb mRNA ( Figure 2A) as well as protein expression ( Figures 2B, C) was restored to normal levels. As patients with LAM disease are treated with rapamycin, and rapamycin is known to downregulate RARb, RARb protein expression levels were quantified in patient derived angiomyolipoma and LAM lung cell lines after 10 nM rapamycin treatment in the presence or absence of 2 mM RA ( Figures 2D-G). While 10 nM rapamycin mono treatment had no effect on RARb levels, 2 mM RA increased RARb expression even in combination with rapamycin in the TSC2-/-cell lines ( Figures 2D-G). The effects of the above treatments were tested on mTOR activity in the angiomyolipoma cell line S102 and its control S103 by western blotting of S6 and pS6 proteins ( Figure 2F). While 10 nM rapamycin significantly reduced S6 phosphorylation close to control levels ( Figures 2F, G), pS6 levels in the presence of 2 mM RA mono treatment was not affected and remained just as high as in the untreated TSC-/control. Combination treatment with 10 nM rapamycin and 2 mM RA resulted in middle ground. Significantly increased but not fully enhanced RARb protein expression and significantly reduced pS6 levels but not as low as in the presence of 10 nM rapamycin mono treatment (Figures 2D-G).
Based on the data TSC mutation affects downstream signals including the vitamin A metabolic enzyme signalling cascades ( Figure 3A). As the FDA approved rapamycin and RA in combination restored RARb and pS6 levels we also tested both drugs on vitamin A metabolic enzyme expression and activity. Mono treatment with 2 mM RA normalised mRNA expression levels of ADH (1A, 4) and ALDH (1A1, 1A2, 1A3) ( Figure 3B). Also, in RA treated TSC mutant S102 and primary LAM lung derived cell lines ADH and ALDH enzymes activity showed significant decrease compared to untreated controls ( Figure 3B). Expression levels ( Figure 3B) and enzymatic activity (Figures 3C-F) of metabolic enzymes were also quantified after 10 and 20 nM rapamycin and/or 2 mM RA treatments. The cultures were assessed after 24 h incubation. While in mono treatment the 20 nM rapamycin was the most efficient in reducing ALDH (35) and ADH activity, combination treatment of 10 nM rapamycin and 2 mM RA stabilised mRNA expression and activity of ADH and ALDH the most closely to TSC2+/+ control levels ( Figures 3B-F).
To test whether normalization of enzyme levels and activity in vitamin A metabolism and suppression of mTOR activity would have an effect on cellular proliferation and migration, the effect of 2 mM RA in combination with 10 nM rapamycin were tested in mono and combination treatment in a scratch and a BrdU assay (36,37). The combined treatment of TSC2-/-cell lines with rapamycin (10 nM) and RA (2 mM) decreased cellular migration significantly ( Figures 4A, B). Furthermore, the combination significantly decreased the proliferation capacity detected in BrdU assay compared to rapamycin mono treatment ( Figures 4C, D).
Apart from increased cell migration and proliferation, TSCdeficiency is characterized by structural changes of the affected tissues. Such changes cannot be detected in traditional 2D cell cultures, therefore a 3D tissue aggregates were used (27). The 3D aggregate tissues containing patient derived LAM lung cell lines developed empty sac formations after 24 h incubation which feature was reduced after 10 nM rapamycin and/or 2 mM RA treatment making the LAM cell containing co-cultures structurally similar to the aggregate cultures containing only TSC+/+ BSMC and NHLF cells ( Figure 4E). Additionally, 10 nM rapamycin and/or 2 mM RA treatments increased RARb protein expression even in the 3D tissue structures containing TSC mutant cell lines (S. Figure 3).

DISCUSSION
In our previous study of LAM, we detected correlation between mTOR activation, mitochondrial dysfunction and downregulation of the proliferation suppressor nuclear receptor family of RAR and RXR (6). Recent studies have also shown that rapamycin treatment induced upregulation of miR-29b in LAM affected cell growth, migration, and invasion via regulation of RARb activity (19).
In the present study, we confirmed that downregulation of RARb is not just a feature of TSC-deficient cell lines (angiomyolipoma, LAM primary cell lines) but it is characteristically present in primary LAM lung tissue sections ( Figures 1D-F). In many cancers (38) the activity of RARb itself is suppressed via various pathways leading up to mTOR activation (19,39). As RARb levels are strongly associated with alterations in the vitamin A metabolic pathway (11), clear understanding of vitamin A metabolism in connection with TSC mutation is important for better disease control.
In the present study, we used TSC mutant angiomyolipoma and primary LAM lung derived cell lines pre-dating the rapamycin era to investigate enzyme expression and activity responsible for retinol metabolism. Based on our study the ability to metabolise retinol is seriously compromised in TSC-deficient cells (Figure 1). Many enzymes, including ADH1A, ADH1B, ADH1C ADH6, ALDH1A2, ALDH1A3, and ALDH3A1 were drastically upregulated, while others including ADH4, ALDH1A1, ALDH3B1, ALDH3B2, ALDH4A1 and ALDH5A1 were significantly downregulated ( Figure 1). The characteristic function of ALDHs is to oxidize aldehydes that would otherwise participate in signalling pathways to induce cellular, to minimize ROS production and to mediate RA signalling cascades (40). Other studies have also shown that in diseases caused by TSC mutation which increases mTORC1 activity is associated with deregulation of ALDH expression and activity, resistance to oxidative stress, greater proliferation, migration, and invasion as well as higher levels of VEGF expression (32,35). These regulatory mechanisms are important in regulation of proliferation, tumorigenesis and resistance to therapy (41). Expression of ALDHs are also regulated by RA compounds including the chemotherapeutic vitamin A or chemically related molecules (retinoids) as well as oncogenic pathways including the WNT/bcatenin and the MUC1-C/ERK pathways (40). CYP2E1 degrades retinoic acid (RA) and retinol to polar metabolites with toxic and apoptotic properties (42). Imbalance in the level of alcohol dehydrogenases acts as a competitive inhibitor of retinol oxidation in the liver which may reduce the biosynthesis of retinoic acid (43). It is especially important that co-expression and physical interactions amongst the metabolic enzymes of retinol are tightly controlled and important in regulation of cellular differentiation, proliferation, and migration. Our experiments have highlighted that patients might benefit from combination of RA with the routinely used treatment of rapamycin in diseases affected by TSC mutation. In such treatment, reduction of rapamycin dosage and closely normalised vitamin A metabolic enzyme activities ( Figure 3) could lead to beneficial physiological effects including reduced cellular proliferation and migration ( Figure 4).

CONCLUSION
Importantly, several enzymes of the vitamin A metabolism and the nuclear receptor RARb can become potential therapeutic targets in TSC mutant or deregulated neoplasms (44,45). RA for example is an FDA approved drug for acute myeloid leukaemia as RA can normalize RARb levels and limit cancer cell migration and consequent disease progression (45). Based on our study we propose that clinical assessment of the combination of RA with reduced dosage of rapamycin might limit adverse reactions to rapamycin in rapamycin sensitive tuberous sclerosis, LAM and angiomyolipoma patients. With reduction of rapamycin levels, the inhibitory effect of rapamycin on ALDH can also become limited which allows better balance in vitamin A metabolism and consequently in RARb activity. Increased expression and activity of RARb might also lead to inhibition of cellular migration, .0002 and P<0.0001, respectively). (C, D) Proliferation capacity of S102 compared to S103 using BrdU assay (BrdU green, DAPI blue, size-bar 100, 50, 25 mm).
Proliferation ratio compared to untreated S103 ± technical error of replicates (t-test). Significant changes are marked as ★, ★★ and ★★★ (P<0.05, P<0.001 and P<0.0002 respectively). (E) Empty sac formation in NHLF-LAM co-cultures compared to NHLF-BSMC co-cultures in the presence or absence of 10 nM rapamycin and/or 2 µM RA treatment (24 h). Empty sac formation is marked with white circles in the staining where RARb is red, NHLF-GFP is green and the nucleus is stained by DAPI (blue).
proliferation and as a result improved disease control. Further studies of improved drug concentrations and clinical assessment of our in vitro results are certainly required to modify treatment strategies for patients suffering from diseases affected by TSC mutations.

DATA AVAILABILITY STATEMENT
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

ETHICS STATEMENT
The study was approved by the Medical Research Council of Hungary (54034-4/2018/EKU). Written informed consent for participation was not required for this study in accordance with the national legislation and the institutional requirements.

AUTHOR CONTRIBUTIONS
EA and JB-B: performed the experiments, isolated RNA and protein from NHLF, SMC and LAM, cellular staining, embedding of samples for microscopy, performed data analysis, and prepared